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Title: Comparative genomics and prediction of conditionally dispensable sequences in legume-infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors

Author
item WILLIAMS, ANGELA - University Of Western Australia
item SHARMA, MAMTA - International Crops Research Institute For The Semi-Arid Tropics (ICRISAT)
item THATCHER, LOUISE - Commonwealth Scientific And Industrial Research Organisation (CSIRO)
item AZAM, SARWAR - International Crops Research Institute For The Semi-Arid Tropics (ICRISAT)
item HANE, JAMES - Curtin University
item KIDD, BRENDAN - Commonwealth Scientific And Industrial Research Organisation (CSIRO)
item ANDERSON, JONATHAN - University Of Western Australia
item GHOSH, RAJU - International Crops Research Institute For The Semi-Arid Tropics (ICRISAT)
item GARG, GAGAN - Commonwealth Scientific And Industrial Research Organisation (CSIRO)
item LICHTENZVEIG, JUDITH - Curtin University
item Kistler, Harold
item SHEA, TERRANCE - Broad Institute Of Mit/harvard
item YOUNG, SARAH - Broad Institute Of Mit/harvard
item BUCK, SALLY-ANNE - Commonwealth Scientific And Industrial Research Organisation (CSIRO)
item KAMPHUIS, LARS - University Of Western Australia
item SAXENA, RACHIT - International Crops Research Institute For The Semi-Arid Tropics (ICRISAT)
item PANDE, SURESH - International Crops Research Institute For The Semi-Arid Tropics (ICRISAT)
item MA, LI-JUN - University Of Massachusetts
item VARSHNEY, RAJEEV - International Crops Research Institute For The Semi-Arid Tropics (ICRISAT)
item SINGH, KARAM - University Of Western Australia

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/17/2016
Publication Date: 3/1/2016
Citation: Williams, A.H., Sharma, M., Thatcher, L.F., Azam, S., Hane, J.K., Kidd, B., Anderson, J.A., Ghosh, R., Garg, G., Lichtenzveig, J., Kistler, H.C., Shea, T., Young, S., Buck, S.G., Kamphuis, L.G., Saxena, R., Pande, S., Ma, L., Varshney, R.K., Singh, K. 2016. Comparative genomics and prediction of conditionally dispensable sequences in legume-infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors. Biomed Central (BMC) Genomics. 17(191):1-24. doi: 10.1186/s12864-016-2486-8.

Interpretive Summary: Soil-borne fungi called Fusarium oxysporum cause devastating wilt disease on many crops including legumes that supply human dietary protein needs across many parts of the globe. We present and compare draft genome assemblies for three legume-infecting strains including two that are significant pathogens of chickpea and pea, the world’s second and third most important grain legumes, and another that infects alfala for which we developed a model legume pathosystem utilizing the alfalfa relative Medicago truncatula.

Technical Abstract: Focusing on the identification of pathogenicity gene content, we leveraged the reference genomes of Fusarium pathogens F. oxysporum f. sp. lycopersici (tomato-infecting) and F. solani (pea-infecting) and their well-characterised core and dispensable chromosomes to predict genomic organisation in the newly sequenced legume-infecting isolates. Dispensable chromosomes are not essential for growth and in Fusarium species are known to be enriched in host-specificity and pathogenicity-associated genes. Comparative genomics of the publically available Fusarium species revealed differential patterns of sequence conservation across F. oxysporum formae speciales, with legume-pathogenic formae speciales not exhibiting greater sequence conservation between them relative to non-legume formae speciales, possibly indicating the lack of a common ancestral source for legume pathogenicity. Combining predicted dispensable gene content with in planta expression in the model legume-infecting isolate, we identified smaller conserved regions and candidate effectors, four of which shared greatest similarity to proteins from another legume-infecting ff. spp.